MATLAB: Fill a gap on an image surface

binarycurve fittingedgeImage Processing Toolboximage segmentation

Hello,
I have an image as follows:
bone_image.jpg
I am using activecontour to detect the edges of the bone.
function [bw] = segmentBone(imageFile)
%Function for segmenting the bone from the background
imageFile = imageFile(:,:,1);
mask_width = 1;
border_width = 2;
imageFile = padarray(imageFile, [border_width, border_width], 0);
mask = zeros(size(imageFile));
mask(mask_width:end-mask_width,mask_width:end-mask_width) = 1;
small_image_itter = 651;
bw = activecontour(imageFile, mask, small_image_itter, 'Chan-Vese', 'SmoothFactor', 0.95);
end
This is the result I get:
segmented_bone.jpeg
The issue is that crack in the middle of the bone. I want to flatten it, so that the lower surface looks smooth. This is an example of what I want to achieve:
segmented_bone_flattened.jpg
It is really important that the boundaries of the bone stay the same and do not get thicker!
Any ideas on how to solve this task?
Thanks in advance!

Best Answer

Can you threshold it? If that gives an OK boundary except for that gap, then use the boundary() function.
Try this:
clc; % Clear the command window.
clear all;
close all; % Close all figures (except those of imtool.)
workspace; % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 16;
%===============================================================================
% Get the name of the image the user wants to use.
baseFileName = 'bone_image.jpeg';
folder = pwd;
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
% The file doesn't exist -- didn't find it there in that folder.
% Check the entire search path (other folders) for the file by stripping off the folder.
fullFileNameOnSearchPath = baseFileName; % No path this time.
if ~exist(fullFileNameOnSearchPath, 'file')
% Still didn't find it. Alert user.
errorMessage = sprintf('Error: %s does not exist in the search path folders.', fullFileName);
uiwait(warndlg(errorMessage));
return;
end
end
%=======================================================================================
% Read in demo image.
grayImage = imread(fullFileName);
% Get the dimensions of the image.
[rows, columns, numberOfColorChannels] = size(grayImage)
if numberOfColorChannels > 1
grayImage = rgb2gray(grayImage);
end
% Display image.

subplot(2, 2, 1);
imshow(grayImage, []);
impixelinfo;
axis on;
caption = sprintf('Original Image\n%s', baseFileName);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo(); % Set up status line to see values when you mouse over the image.
% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0.05 1 0.95]);
% Get rid of tool bar and pulldown menus that are along top of figure.
% set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off')
drawnow;
% Crop off white frame surrounding the image.
grayImage = grayImage(5:645, 6:647);
%===================================================================================
% Get a histogram
subplot(2, 2, 2);
histogram(grayImage);
grid on;
title('Histogram of gray scale image', 'FontSize', fontSize, 'Interpreter', 'None');
% Convert to binary
% binaryImage = imbinarize(grayImage);
binaryImage = grayImage > 50;
% Fill blob and take the largest one.
binaryImage = bwareafilt(imfill(binaryImage, 'holes'), 1);
% Display image.
subplot(2, 2, 3);
imshow(binaryImage, []);
impixelinfo;
axis on;
title('Original Boundary', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
% Get outline
boundaries = bwboundaries(binaryImage);
x = boundaries{1}(:, 2);
y = boundaries{1}(:, 1);
hold on;
plot(x, y, 'r-', 'LineWidth', 3);
% Get the boundary
b = boundary(x, y, 0.9);
subplot(2, 2, 4);
imshow(binaryImage);
hold on;
plot(x(b), y(b), 'r-', 'LineWidth', 3);
axis image; % Make sure image is not artificially stretched because of screen's aspect ratio.
caption = sprintf('Boundary without Gap.');
title(caption, 'FontSize', fontSize);
0000 Screenshot.png